ArticleJournal of chemical theory and computation2011
IDSite: An accurate approach to predict P450-mediated drug metabolism.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 76 citations in OpenAlex.
- MetaCYP: a unified framework for prediction of cytochrome P450 metabolic sites and reaction types via multimodal deep learning.Frontiers in chemistry · 2026Article
- Metabolite Identification Data in Drug Discovery, Part 2: Site-of-Metabolism Annotation, Analysis, and Exploration for Machine Learning.Molecular pharmaceutics · 2025Article
- Metabolite Identification Data in Drug Discovery, Part 1: Data Generation and Trend Analysis.Molecular pharmaceutics · 2025Article
- Artificial intelligence and computational methods in human metabolism research: A comprehensive survey.Journal of pharmaceutical analysis · 2025Review
- Automated Annotation of Sites of Metabolism from Biotransformation Data.Journal of chemical information and modeling · 2025Article
- Conformational Plasticity Enhances the Brain Penetration of a Metabolically Stable, Dual-Functional Opioid-Peptide CycloAnt.International journal of molecular sciences · 2024Article
- Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation.Journal of chemical information and modeling · 2024Article
- D-CyPre: a machine learning-based tool for accurate prediction of human CYP450 enzyme metabolic sites.PeerJ. Computer science · 2024Article
- QSAR analysis of 3-pyrimidin-4-yl-oxazolidin-2-one derivatives isocitrate dehydrogenase inhibitors using Topomer CoMFA and HQSAR methods.Molecular diversity · 2022Article
- Impact of Established and Emerging Software Tools on the Metabolite Identification Landscape.Frontiers in toxicology · 2022Article
- Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA.BMC bioinformatics · 2021Article
- NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism.eLife · 2021Article
- Computational methods and tools to predict cytochrome P450 metabolism for drug discovery.Chemical biology & drug design · 2019Review
- RD-Metabolizer: an integrated and reaction types extensive approach to predict metabolic sites and metabolites of drug-like molecules.Chemistry Central journal · 2017Article
- Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics.Journal of cheminformatics · 2016Article
- Predicting drug metabolism: experiment and/or computation?Nature reviews. Drug discovery · 2015Review
- Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates.Pharmaceutical research · 2015Article
- Article
- Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software.Future medicinal chemistry · 2012Article
- RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes.Journal of chemical information and modeling · 2012Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.